ARBA00089175 vacuolar localization (GO:1990849)

id: ARBA00089175
description: >-
  ARBA rule assigning GO:1990849 vacuolar localization to eukaryotic proteins that carry two CATH
  FunFams named for pleckstrin homology domain-containing family M member 1 (PLEKHM1).
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00089175
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 1.20.58.900:FF:000013
      curie: CATH.FunFam:1.20.58.900:FF:000013
      label: pleckstrin homology domain-containing family M member 1 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 2.30.29.30:FF:000315
      curie: CATH.FunFam:2.30.29.30:FF:000315
      label: pleckstrin homology domain-containing family M member 1 isoform X1
      negated: false
    - condition_type: TAXON
      value: '2759'
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      Both FunFams are named for PLEKHM1 and co-occur in the same three Swiss-Prot proteins: human,
      mouse and rat PLEKHM1 (Q9Y4G2, Q7TSI1, Q5PQS0). In all of UniProtKB the conjunction matches
      116 proteins, all in Metazoa.
    pairwise_overlap:
    - condition_a: 1.20.58.900:FF:000013
      condition_b: 2.30.29.30:FF:000315
      protein_database: SWISSPROT
      count_a: 3
      count_b: 3
      intersection_count: 3
      a_minus_b_count: 0
      b_minus_a_count: 0
      jaccard_similarity: 1.0
      containment_a_in_b: 1.0
      containment_b_in_a: 1.0
      interpretation: REDUNDANT
  go_annotations:
  - go_id: GO:1990849
    go_label: vacuolar localization
    aspect: BP
  entries:
  - id: 1.20.58.900:FF:000013
    type: FUNFAM
    label: pleckstrin homology domain-containing family M member 1 isoform X1
    appears_in_condition_sets:
    - 1
    protein_count: 3
    related_entries:
    - relationship: EQUIV
      target_id: 2.30.29.30:FF:000315
      containment: 1.0
      jaccard_similarity: 1.0
      intersection_count: 3
      exclusive_count: 0
    - relationship: PREDICTS
      target_id: GO:1990849
      containment: 1.0
      jaccard_similarity: 0.01
      intersection_count: 3
      exclusive_count: 0
  - id: 2.30.29.30:FF:000315
    type: FUNFAM
    label: pleckstrin homology domain-containing family M member 1 isoform X1
    appears_in_condition_sets:
    - 1
    protein_count: 3
    related_entries:
    - relationship: EQUIV
      target_id: 1.20.58.900:FF:000013
      containment: 1.0
      jaccard_similarity: 1.0
      intersection_count: 3
      exclusive_count: 0
    - relationship: PREDICTS
      target_id: GO:1990849
      containment: 1.0
      jaccard_similarity: 0.01
      intersection_count: 3
      exclusive_count: 0
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2025-03-21'
  modified_date: '2026-05-04'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 1
review_summary: >-
  The single condition set was examined. It matches 116 UniProtKB proteins, all metazoan, including
  human, mouse and rat PLEKHM1. Human and mouse PLEKHM1 are experimentally annotated to GO:0032418
  lysosome localization, which is an is_a child of the rule's term GO:1990849. The rule is therefore
  correct for what it matches but asserts the parent of the term the evidence supports.
action: MODIFY
action_rationale: >-
  The matched family is PLEKHM1 in animals, where the organelle is the lysosome and the experimental
  annotations are to lysosome localization. No matched protein lies outside Metazoa, so the generic
  vacuolar term gains nothing.
suggested_modifications:
- >-
  Replace the consequent GO:1990849 vacuolar localization with its child GO:0032418 lysosome localization.
parsimony:
  assessment: ACCEPTABLE
  notes: >-
    The two FunFams co-occur in the same three Swiss-Prot proteins (recorded Jaccard 1.0), so the
    second adds no discrimination there; it does no harm.
literature_support:
  assessment: STRONG
  notes: >-
    Curated experimental annotations on the matched proteins: human PLEKHM1 (Q9Y4G2) GO:0032418 lysosome
    localization, IDA, PMID:28325809; mouse Plekhm1 (Q7TSI1) GO:0032418, IMP, PMID:27777970.
condition_overlap:
  assessment: COMPLETE
  notes: >-
    There is one condition set. Its two FunFam conditions match the same three Swiss-Prot proteins.
go_specificity:
  assessment: TOO_BROAD
  notes: >-
    GO:1990849 is the parent of GO:0032418 lysosome localization, the term the experimental annotations
    use.
taxonomic_scope:
  assessment: APPROPRIATE
  notes: >-
    The Eukaryota condition does not exclude anything: all 116 UniProtKB matches of the two FunFams
    are metazoan.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:1990849
  label: vacuolar localization
  assessment: TOO_GENERAL
  matched_protein_count: 116
  correct_examples:
  - Q9Y4G2
  - Q7TSI1
  - Q5PQS0
  notes: >-
    UniProtKB query xref funfam-1.20.58.900:FF:000013 AND funfam-2.30.29.30:FF:000315 (2026-11-09):
    116 entries, 3 reviewed, 0 outside taxonomy 33208 (Metazoa). QuickGO: Q9Y4G2 GO:0032418 IDA PMID:28325809;
    Q7TSI1 GO:0032418 IMP PMID:27777970; Q5PQS0 GO:0032418 ISS and ISO. GO:0032418 lysosome localization
    is_a GO:1990849.
confidence: 0.7
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    PLEKHM1 orthologues exist throughout fungal, plant and animal lineages and yeast has functional
    homologues, so the generic vacuolar term suits cross-eukaryotic application.
  correction: >-
    Every protein the rule matches is metazoan. The supporting passage came from generated research
    notes and described phenotypic similarity of yeast vps mutants, not homology.
  error_type: TAXON_MISREAD
  evidence:
  - 'UniProtKB query for both FunFams AND NOT taxonomy 33208: 0 entries (116 in total)'
- date: '2026-11-10'
  withdrawn_claim: GO:1990849 is the appropriate term.
  correction: >-
    The experimental annotations of the matched proteins are to the child term GO:0032418 lysosome
    localization.
  error_type: GENERAL_IS_NOT_WRONG
  evidence:
  - 'QuickGO: Q9Y4G2 GO:0032418 IDA PMID:28325809'
  - 'QuickGO: Q7TSI1 GO:0032418 IMP PMID:27777970'
  - 'QuickGO: GO:0032418 is_a GO:1990849'
- date: '2026-11-10'
  withdrawn_claim: Literature support is strong, as shown by deep-research summaries.
  correction: >-
    The summaries were generated notes, not checked publications. The support recorded now is the
    curated experimental GO annotation of the matched proteins.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - Previous supported_by cited ARBA00089175-deep-research-perplexity.md and -falcon.md only